[2024-01-24 11:26:38,595] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:38,597] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:38,598] [INFO] DQC Reference Directory: /var/lib/cwl/stg372d1cff-8b1d-48cc-b778-12dbd0edf243/dqc_reference
[2024-01-24 11:26:39,909] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:39,910] [INFO] Task started: Prodigal
[2024-01-24 11:26:39,910] [INFO] Running command: gunzip -c /var/lib/cwl/stgd9908190-9373-4d5d-8447-d6c79fc1d16e/GCF_006539065.1_ASM653906v1_genomic.fna.gz | prodigal -d GCF_006539065.1_ASM653906v1_genomic.fna/cds.fna -a GCF_006539065.1_ASM653906v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:58,886] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:58,886] [INFO] Task started: HMMsearch
[2024-01-24 11:26:58,886] [INFO] Running command: hmmsearch --tblout GCF_006539065.1_ASM653906v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg372d1cff-8b1d-48cc-b778-12dbd0edf243/dqc_reference/reference_markers.hmm GCF_006539065.1_ASM653906v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:59,205] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:59,206] [INFO] Found 6/6 markers.
[2024-01-24 11:26:59,256] [INFO] Query marker FASTA was written to GCF_006539065.1_ASM653906v1_genomic.fna/markers.fasta
[2024-01-24 11:26:59,256] [INFO] Task started: Blastn
[2024-01-24 11:26:59,256] [INFO] Running command: blastn -query GCF_006539065.1_ASM653906v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg372d1cff-8b1d-48cc-b778-12dbd0edf243/dqc_reference/reference_markers.fasta -out GCF_006539065.1_ASM653906v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:59,843] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:59,846] [INFO] Selected 10 target genomes.
[2024-01-24 11:26:59,847] [INFO] Target genome list was writen to GCF_006539065.1_ASM653906v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:59,854] [INFO] Task started: fastANI
[2024-01-24 11:26:59,854] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9908190-9373-4d5d-8447-d6c79fc1d16e/GCF_006539065.1_ASM653906v1_genomic.fna.gz --refList GCF_006539065.1_ASM653906v1_genomic.fna/target_genomes.txt --output GCF_006539065.1_ASM653906v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:09,515] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:09,516] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg372d1cff-8b1d-48cc-b778-12dbd0edf243/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:09,516] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg372d1cff-8b1d-48cc-b778-12dbd0edf243/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:09,528] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:27:09,528] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:09,528] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Brevibacillus parabrevis	strain=NBRC 12334	GCA_006539065.1	54914	54914	type	True	100.0	1933	1938	95	conclusive
Brevibacillus parabrevis	strain=NRRL NRS 605	GCA_003710905.1	54914	54914	type	True	99.9991	1936	1938	95	conclusive
Brevibacillus agri	strain=NBRC 15538	GCA_006540025.1	51101	51101	type	True	85.3774	1323	1938	95	below_threshold
Brevibacillus agri	strain=NRRL NRS 1219	GCA_003710885.1	51101	51101	type	True	85.3596	1341	1938	95	below_threshold
Brevibacillus agri	strain=DSM 6348	GCA_004117055.1	51101	51101	type	True	85.3195	1377	1938	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:09,530] [INFO] DFAST Taxonomy check result was written to GCF_006539065.1_ASM653906v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:09,531] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:09,531] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:09,532] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg372d1cff-8b1d-48cc-b778-12dbd0edf243/dqc_reference/checkm_data
[2024-01-24 11:27:09,534] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:09,591] [INFO] Task started: CheckM
[2024-01-24 11:27:09,592] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006539065.1_ASM653906v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006539065.1_ASM653906v1_genomic.fna/checkm_input GCF_006539065.1_ASM653906v1_genomic.fna/checkm_result
[2024-01-24 11:28:04,620] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:04,622] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:04,647] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:04,647] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:04,648] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006539065.1_ASM653906v1_genomic.fna/markers.fasta)
[2024-01-24 11:28:04,648] [INFO] Task started: Blastn
[2024-01-24 11:28:04,649] [INFO] Running command: blastn -query GCF_006539065.1_ASM653906v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg372d1cff-8b1d-48cc-b778-12dbd0edf243/dqc_reference/reference_markers_gtdb.fasta -out GCF_006539065.1_ASM653906v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:05,454] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:05,459] [INFO] Selected 13 target genomes.
[2024-01-24 11:28:05,459] [INFO] Target genome list was writen to GCF_006539065.1_ASM653906v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:05,482] [INFO] Task started: fastANI
[2024-01-24 11:28:05,482] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9908190-9373-4d5d-8447-d6c79fc1d16e/GCF_006539065.1_ASM653906v1_genomic.fna.gz --refList GCF_006539065.1_ASM653906v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006539065.1_ASM653906v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:21,858] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:21,882] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:21,882] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_003710905.1	s__Brevibacillus parabrevis	99.9991	1936	1938	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.83	96.13	0.96	0.94	7	conclusive
GCF_004117055.1	s__Brevibacillus agri	85.3353	1375	1938	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	99.52	99.18	0.94	0.89	8	-
GCF_003710935.1	s__Brevibacillus gelatini	84.0941	1150	1938	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003013405.1	s__Brevibacillus formosus	80.3758	870	1938	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.07	95.45	0.94	0.90	6	-
GCF_003013475.1	s__Brevibacillus porteri	80.3723	856	1938	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	97.63	95.52	0.90	0.88	7	-
GCF_005217615.1	s__Brevibacillus antibioticus	80.3603	804	1938	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000010165.1	s__Brevibacillus brevis_D	80.2279	851	1938	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	97.35	96.52	0.92	0.90	11	-
GCF_013284355.1	s__Brevibacillus sp013284355	80.2233	859	1938	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001039275.2	s__Brevibacillus brevis_C	80.2174	880	1938	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.38	97.50	0.95	0.94	3	-
GCF_000282075.1	s__Brevibacillus sp000282075	80.2072	834	1938	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	96.13	96.13	0.92	0.92	2	-
GCF_002897295.1	s__Brevibacillus reuszeri_A	79.9991	765	1938	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	96.18	96.18	0.89	0.89	2	-
GCF_001420695.1	s__Brevibacillus choshinensis	79.6828	650	1938	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016811915.1	s__Brevibacillus choshinensis_A	79.5674	702	1938	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:21,884] [INFO] GTDB search result was written to GCF_006539065.1_ASM653906v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:21,885] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:21,888] [INFO] DFAST_QC result json was written to GCF_006539065.1_ASM653906v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:21,889] [INFO] DFAST_QC completed!
[2024-01-24 11:28:21,889] [INFO] Total running time: 0h1m43s